scholarly journals Direct inference of the distribution of fitness effects of spontaneous mutations in Chlamydomonas reinhardtii

2019 ◽  
Author(s):  
Katharina B. Böndel ◽  
Susanne A. Kraemer ◽  
Tobias S. Samuels ◽  
Deirdre McClean ◽  
Josianne Lachapelle ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Chlamydomonas Reinhardtii ◽  
Spontaneous Mutation ◽  
Evolutionary Process ◽  
Cumulative Effect ◽  
Neutral Evolution ◽  
Spontaneous Mutations ◽  
Effective Population ◽  
Fitness Effects ◽  
Bayesian Mixture

AbstractSpontaneous mutations are the source of new genetic variation and are thus central to the evolutionary process. In molecular evolution and quantitative genetics, the nature of genetic variation depends critically on the distribution of fitness effects (DFE) of mutations. Spontaneous mutation accumulation (MA) experiments have been the principal approach for investigating the overall rate of occurrence and cumulative effect of mutations, but have not allowed the effects of individual mutations to be studied directly. Here, we crossed MA lines of the green alga Chlamydomonas reinhardtii with its unmutated ancestral strain to create haploid recombinant lines, each carrying an average of 50% of the accumulated mutations in a variety of combinations. With the aid of the genome sequences of the MA lines, we inferred the genotypes of the mutations, assayed their growth rate as a measure of fitness, and inferred the DFE using a novel Bayesian mixture model that allows the effects of individual mutations to be estimated. We infer that the DFE is highly leptokurtic (L-shaped), and that a high proportion of mutations increase fitness in the laboratory environment. The inferred distribution of effects for deleterious mutations is consistent with a strong role for nearly neutral evolution. Specifically, such a distribution predicts that nucleotide variation and genetic variation for quantitative traits will be insensitive to change in the effective population size.

scholarly journals The distribution of fitness effects of spontaneous mutations in Chlamydomonas reinhardtii inferred using frequency changes under experimental evolution

2021 ◽  
Author(s):  
Katharina B. Böndel ◽  
Toby Samuels ◽  
Rory J. Craig ◽  
Rob W. Ness ◽  
Nick Colegrave ◽  
...  
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Experimental Evolution ◽  
Spontaneous Mutations ◽  
Negative Effects ◽  
Serial Transfer ◽  
Fitness Effects ◽  
Markov Chain Method ◽  
Bayesian Monte Carlo ◽  
High Fraction ◽  
Frequency Changes

The distribution of fitness effects (DFE) for new mutations is fundamental for many aspects of population and quantitative genetics. In this study, we have inferred the DFE in the single-celled alga Chlamydomonas reinhardtii by estimating changes in the frequencies of 254 spontaneous mutations under experimental evolution and equating the frequency changes of linked mutations with their selection coefficients. We generated seven populations of recombinant haplotypes by crossing seven independently derived mutation accumulation lines carrying an average of 36 mutations in the homozygous state to a mutation-free strain of the same genotype. We then allowed the populations to evolve under natural selection in the laboratory by serial transfer in liquid culture. We observed substantial and repeatable changes in the frequencies of many groups of linked mutations, and, surprisingly, as many mutations were observed to increase as decrease in frequency. We developed a Bayesian Monte Carlo Markov Chain method to infer the DFE. This computes the likelihood of the observed distribution of changes of frequency, and obtains the posterior distribution of the selective effects of individual mutations, while assuming a two-sided gamma distribution of effects. We infer that the DFE is a highly leptokurtic distribution, and that approximately equal proportions of mutations have positive and negative effects on fitness. This result is consistent with what we have observed in previous work on a different C. reinhardtii strain, and suggests that a high fraction of new spontaneously arisen mutations are advantageous in a simple laboratory environment.

scholarly journals Inferring the distribution of fitness effects of spontaneous mutations in Chlamydomonas reinhardtii

PLoS Biology ◽  
2019 ◽  
Vol 17 (6) ◽  
pp. e3000192 ◽  
Author(s):  
Katharina B. Böndel ◽  
Susanne A. Kraemer ◽  
Toby Samuels ◽  
Deirdre McClean ◽  
Josianne Lachapelle ◽  
...  
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Spontaneous Mutations ◽  
Fitness Effects

scholarly journals Nearly Neutral Evolution Across the Drosophila melanogaster Genome

2017 ◽  
Author(s):  
David Castellano ◽  
Jennifer James ◽  
Adam Eyre-Walker
Keyword(s):  
Drosophila Melanogaster ◽  
Neutral Theory ◽  
Neutral Evolution ◽  
Effective Population ◽  
Synonymous Mutations ◽  
Fitness Effects ◽  
Independent Estimate ◽  
Polymorphism Data ◽  
Neutral Mutations ◽  
The Relationship

AbstractUnder the nearly neutral theory of molecular evolution the proportion of effectively neutral mutations is expected to depend upon the effective population size (Ne). Here we investigate whether this is the case across the genome of Drosophila melanogaster using polymorphism data from North American and African lines. We show that the ratio of the number of non-synonymous and synonymous polymorphisms is negatively correlated to the number of synonymous polymorphisms, even when the non-independence is accounted for. The relationship is such that the proportion of effectively neutral non-synonymous mutations increases by ~45% as Ne is halved. However, we also show that this relationship is steeper than expected from an independent estimate of the distribution of fitness effects from the site frequency spectrum. We investigate a number of potential explanations for this and show, using simulation, that this is consistent with a model of genetic hitch-hiking: genetic hitch-hiking depresses diversity at neutral and weakly selected sites, but has little effect on the diversity of strongly selected sites.

scholarly journals Inherited Differences in Crossing Over and Gene Conversion Frequencies Between Wild Strains of Sordaria fimicola From “Evolution Canyon”

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1573-1593
Author(s):  
Muhammad Saleem ◽  
Bernard C Lamb ◽  
Eviatar Nevo
Keyword(s):  
Genetic Variation ◽  
Gene Conversion ◽  
Spontaneous Mutation ◽  
Crossing Over ◽  
Natural Genetic Variation ◽  
Evolution Canyon ◽  
Wild Strains ◽  
Sordaria Fimicola ◽  
First And Second Generation ◽  
Consistent Direction

Abstract Recombination generates new combinations of existing genetic variation and therefore may be important in adaptation and evolution. We investigated whether there was natural genetic variation for recombination frequencies and whether any such variation was environment related and possibly adaptive. Crossing over and gene conversion frequencies often differed significantly in a consistent direction between wild strains of the fungus Sordaria fimicola isolated from a harsher or a milder microscale environment in “Evolution Canyon,” Israel. First- and second-generation descendants from selfing the original strains from the harsher, more variable, south-facing slope had higher frequencies of crossing over in locus-centromere intervals and of gene conversion than those from the lusher north-facing slopes. There were some significant differences between strains within slopes, but these were less marked than between slopes. Such inherited variation could provide a basis for natural selection for optimum recombination frequencies in each environment. There were no significant differences in meiotic hybrid DNA correction frequencies between strains from the different slopes. The conversion analysis was made using only conversions to wild type, because estimations of conversion to mutant were affected by a high frequency of spontaneous mutation. There was no polarized segregation of chromosomes at meiosis I or of chromatids at meiosis II.

Inherited and Environmentally Induced Differences in Mutation Frequencies Between Wild Strains of Sordaria fimicola From “Evolution Canyon”

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 87-99
Author(s):  
Bernard C Lamb ◽  
Muhammad Saleem ◽  
William Scott ◽  
Nina Thapa ◽  
Eviatar Nevo
Keyword(s):  
Genetic Variation ◽  
Spontaneous Mutation ◽  
The South ◽  
Natural Genetic Variation ◽  
The North ◽  
Ascospore Germination ◽  
Evolution Canyon ◽  
Two Generations ◽  
Wild Strains ◽  
Sordaria Fimicola

Abstract We have studied whether there is natural genetic variation for mutation frequencies, and whether any such variation is environment-related. Mutation frequencies differed significantly between wild strains of the fungus Sordaria fimicola isolated from a harsher or a milder microscale environment in “Evolution Canyon,” Israel. Strains from the harsher, drier, south-facing slope had higher frequencies of new spontaneous mutations and of accumulated mutations than strains from the milder, lusher, north-facing slope. Collective total mutation frequencies over many loci for ascospore pigmentation were 2.3, 3.5 and 4.4% for three strains from the south-facing slope, and 0.9, 1.1, 1.2, 1.3 and 1.3% for five strains from the north-facing slope. Some of this between-slope difference was inherited through two generations of selfing, with average spontaneous mutation frequencies of 1.9% for south-facing slope strains and 0.8% for north-facing slope strains. The remainder was caused by different frequencies of mutations arising in the original environments. There was also significant heritable genetic variation in mutation frequencies within slopes. Similar between-slope differences were found for ascospore germination-resistance to acriflavine, with much higher frequencies in strains from the south-facing slope. Such inherited variation provides a basis for natural selection for optimum mutation rates in each environment.

scholarly journals Fitness Effects of Spontaneous Mutations in Picoeukaryotic Marine Green Algae

2016 ◽  
Vol 6 (7) ◽  
pp. 2063-2071 ◽  
Author(s):  
Marc Krasovec ◽  
Adam Eyre-Walker ◽  
Nigel Grimsley ◽  
Christophe Salmeron ◽  
David Pecqueur ◽  
...  
Keyword(s):  
Green Algae ◽  
Spontaneous Mutations ◽  
Fitness Effects

scholarly journals The Rate of Spontaneous Mutation for Life-History Traits in Caenorhabditis elegans

Genetics ◽  
1999 ◽  
Vol 151 (1) ◽  
pp. 119-129 ◽  
Author(s):  
Larissa L Vassilieva ◽  
Michael Lynch
Keyword(s):  
Life History ◽  
Caenorhabditis Elegans ◽  
Mutation Rate ◽  
Life History Traits ◽  
Deleterious Mutation ◽  
Spontaneous Mutation ◽  
Spontaneous Mutations ◽  
Homozygous State ◽  
Mutational Effect ◽  
Biological Differences

Abstract Spontaneous mutations were accumulated in 100 replicate lines of Caenorhabditis elegans over a period of ∼50 generations. Periodic assays of these lines and comparison to a frozen control suggest that the deleterious mutation rate for typical life-history characters in this species is at least 0.05 per diploid genome per generation, with the average mutational effect on the order of 14% or less in the homozygous state and the average mutational heritability ∼0.0034. While the average mutation rate per character and the average mutational heritability for this species are somewhat lower than previous estimates for Drosophila, these differences can be reconciled to a large extent when the biological differences between these species are taken into consideration.

scholarly journals The genomic landscape of recombination rate variation in Chlamydomonas reinhardtii reveals a pronounced effect of linked selection

2018 ◽  
Author(s):  
Ahmed R. Hasan ◽  
Rob W. Ness
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Recombination Rate ◽  
Natural Populations ◽  
Gc Content ◽  
Sexual Cycle ◽  
Rate Variation ◽  
Effective Population ◽  
Entire Genome ◽  
Recombination Rate Variation ◽  
Linked Selection

AbstractRecombination confers a major evolutionary advantage by breaking up linkage disequilibrium (LD) between harmful and beneficial mutations and facilitating selection. Here, we use genome-wide patterns of LD to infer fine-scale recombination rate variation in the genome of the model green alga Chlamydomonas reinhardtii and estimate rates of LD decay across the entire genome. We observe recombination rate variation of up to two orders of magnitude, finding evidence of recombination hotspots playing a role in the genome. Recombination rate is highest just upstream of genic regions, suggesting the preferential targeting of recombination breakpoints in promoter regions. Furthermore, we observe a positive correlation between GC content and recombination rate, suggesting a role for GC-biased gene conversion or selection on base composition within the GC-rich genome of C. reinhardtii. We also find a positive relationship between nucleotide diversity and recombination, consistent with widespread influence of linked selection in the genome. Finally, we use estimates of the effective rate of recombination to calculate the rate of sex that occurs in natural populations of this important model microbe, estimating a sexual cycle roughly every 770 generations. We argue that the relatively infrequent rate of sex and large effective population size creates an population genetic environment that increases the influence of linked selection on the genome.

scholarly journals The distribution of mutational effects on fitness in Caenorhabditis elegans inferred from standing genetic variation

2020 ◽  
Author(s):  
Kimberly J. Gilbert ◽  
Stefan Zdraljevic ◽  
Daniel E. Cook ◽  
Asher D. Cutter ◽  
Erik C. Andersen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Caenorhabditis Elegans ◽  
Population Size ◽  
Genomic Structure ◽  
Random Mating ◽  
Population Substructure ◽  
C Elegans ◽  
Fitness Effects ◽  
Self Fertilization ◽  
New Mutations

ABSTRACTThe distribution of fitness effects for new mutations is one of the most theoretically important but difficult to estimate properties in population genetics. A crucial challenge to inferring the distribution of fitness effects (DFE) from natural genetic variation is the sensitivity of the site frequency spectrum to factors like population size change, population substructure, and non-random mating. Although inference methods aim to control for population size changes, the influence of non-random mating remains incompletely understood, despite being a common feature of many species. We report the distribution of fitness effects estimated from 326 genomes of Caenorhabditis elegans, a nematode roundworm with a high rate of self-fertilization. We evaluate the robustness of DFE inferences using simulated data that mimics the genomic structure and reproductive life history of C. elegans. Our observations demonstrate how the combined influence of self-fertilization, genome structure, and natural selection can conspire to compromise estimates of the DFE from extant polymorphisms. These factors together tend to bias inferences towards weakly deleterious mutations, making it challenging to have full confidence in the inferred DFE of new mutations as deduced from standing genetic variation in species like C. elegans. Improved methods for inferring the distribution of fitness effects are needed to appropriately handle strong linked selection and selfing. These results highlight the importance of understanding the combined effects of processes that can bias our interpretations of evolution in natural populations.

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